brukerapi 0.2.6__tar.gz → 0.3.0__tar.gz

{brukerapi-0.2.6/brukerapi.egg-info → brukerapi-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brukerapi
-Version: 0.2.6
+Version: 0.3.0
 Summary: Bruker API
 Author-email: Tomas Psorn <tomaspsorn@isibrno.cz>, Jiri Vitous <vitous@isibrno.cz>
 Maintainer-email: Jiri Vitous <vitous@isibrno.cz>
@@ -50,9 +50,9 @@ Load any **data set**:
 .. code-block:: python
 
     from brukerapi.dataset import Dataset
-    dataset = Dataset('{path}/2dseq')    # create data set, works for fid, 2dseq, rawdata.x
+    dataset = Dataset('{path}/2dseq')    # also supports fid, fid_proc.64, traj, and rawdata.jobN
     dataset.data                         # access data array
-    dataset.VisuCoreSize                 # get a value of a single parameter
+    dataset.get_value('VisuCoreSize')    # get a parameter value
 
 Load an entire **study**:
 
@@ -62,17 +62,7 @@ Load an entire **study**:
     study = Study('{path_to_study_folder}')
     dataset = study.get_dataset(exp_id='1', proc_id='1')
 
-    # get_dataset returns an empty dataset
-    # in order to load data into the data set, you can either use the context manager:
-
-    with dataset as d:
-        d.data                         # access data array
-        d.VisuCoreSize                 # get a value of a parameter
-
-    # or the load function
-    dataset.load()
-    dataset.data                       # access data array
-    dataset.VisuCoreSize               # get a value of a single parameter
+    dataset.data                         # Study loads datasets by default
 
 Load a parametric file:
 
@@ -82,8 +72,8 @@ Load a parametric file:
 
    parameters = JCAMPDX('path_to_scan/method')
    
-   TR = data.params["PVM_RepetitionTime"].value # This way
-   TR = data.get_value("PVM_RepetitionTime") # Or this way
+   TR = parameters.params["PVM_RepetitionTime"].value
+   TR = parameters.get_value("PVM_RepetitionTime")
 
 
 
@@ -98,6 +88,8 @@ Features
 * **Random access** for **fid** and **2dseq** data sets
 * **Split** operation implemented over **2dseq** data sets
 * **Filter** operation implemented over Bruker **folders** (allowing you to work with a subset of your study only)
+* ParaVision 5.1, 6.0.1, 7.0.0, and 360 metadata and binary-layout support
+* Metadata-based fallback inference for custom Cartesian, EPI, radial/UTE, spiral, ZTE, CSI, and spectroscopy sequences
 
 Examples
 ========
@@ -127,8 +119,7 @@ From source:
 
     git clone https://github.com/isi-nmr/brukerapi-python.git
     cd brukerapi-python
-    python setup.py build
-    python setup.py install
+    python -m pip install -e .[dev]
 
 Testing
 ========
@@ -137,107 +128,38 @@ data sets:
 
 * `BrukerAPI test data set (Bruker ParaVision v5.1) <https://doi.org/10.5281/zenodo.3899268>`_
 * `BrukerAPI test data set (Bruker ParaVision v6.0.1) <https://doi.org/10.5281/zenodo.3894651>`_
-* `bruker2nifti_qa data set <https://gitlab.com/naveau/bruker2nifti_qa>`_
+* BrukerAPI test data set for ParaVision v7.0.0 (Zenodo DOI collection ``10.5281/zenodo.4522220``)
+* `PV360 standard data <https://github.com/cecilyen/PV360_StdData>`_
+
+The corpus download is opt-in for local runs:
+
+.. code-block:: shell
+
+    python -m pytest test --download_test_data
+
+Without that flag, pytest uses any corpus already present under ``test/test_data`` and
+skips unavailable collections.
+
+File format reference
+=====================
+
+`Bruker ParaVision Raw Data Format
+<https://github.com/gdevenyi/brkraw-legacy/blob/main/FILE_FORMAT.md>`_ is the source of truth
+for file-format parsing, binary layouts, dataset typing, and metadata-driven acquisition
+scheme inference in this project.
 
 Compatibility
 =============
 
-The API was tested using various data sets obtained by **ParaVision 5.1**, **6.0.1** and **360**. It it is compatible
-with the following data set types from individual ParaVision versions.
-
-ParaVision v5.1
-"""""""""""""""
-Compatible data set types:
-
-* **fid**
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
-Compatible pulse sequences for **fid** data sets:
-
-* FLASH.ppg
-* MGE.ppg
-* MSME.ppg
-* RARE.ppg
-* FAIR_RARE.ppg
-* RAREVTR.ppg
-* RAREst.ppg
-* MDEFT.ppg
-* FISP.ppg
-* FLOWMAP.ppg
-* DtiStandard.ppg
-* EPI.ppg
-* FAIR_EPI.ppg
-* DtiEpi.ppg
-* T1_EPI.ppg
-* T2_EPI.ppg
-* T2S_EPI.ppg
-* SPIRAL.ppg
-* DtiSpiral.ppg
-* UTE.ppg
-* UTE3D.ppg
-* ZTE.ppg
-* CSI.ppg
-* FieldMap.ppg
-* NSPECT.ppg
-* PRESS.ppg
-* STEAM.ppg
-* igFLASH.ppg
-
-ParaVision v6.0.1 and v7.0.0
-"""""""""""""""""""""""""""""""
-Compatible data set types:
-
-* **fid**
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
-Compatible pulse sequences for **fid** data sets:
-
-* FLASH.ppg,
-* FLASHAngio.ppg
-* IgFLASH.ppg
-* MGE.ppg
-* MSME.ppg
-* RARE.ppg
-* FAIR_RARE.ppg
-* RAREVTR.ppg
-* RAREst.ppg
-* MDEFT.ppg
-* FISP.ppg
-* FLOWMAP.ppg
-* DtiStandard.ppg
-* EPI.ppg
-* FAIR_EPI.ppg
-* CASL_EPI.ppg
-* DtiEpi.ppg
-* T1_EPI.ppg
-* T2_EPI.ppg
-* T2S_EPI.ppg
-* SPIRAL.ppg
-* DtiSpiral.ppg
-* UTE.ppg
-* UTE3D.ppg
-* ZTE.ppg
-* CSI.ppg
-* FieldMap.ppg
-* SINGLEPULSE.ppg
-* NSPECT.ppg
-* EPSI.ppg
-* PRESS.ppg
-* STEAM.ppg
-* ISIS.ppg
-* CPMG.ppg
-* RfProfile.ppg
-
-
-ParaVision 360 v1.1 v3.0-v3.7
-"""""""""""""""""""""""""""""""""
-Reading rawdata is supported only in a basic form, no reshaping into k-space is supported at the moment.
-Compatible data set types:
-
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
+Tested releases are ParaVision 5.1, 6.0.1, 7.0.0, and PV360 3.x. Supported
+primary binaries are ``fid``, ``fid_proc.64``, ``2dseq``, ``traj``,
+``rawdata.jobN``, and ``rawdata.Navigator``. Known ``fid.spiral``,
+``fid.navFid``, and ``fid.orig`` files are exposed as auxiliary subdatasets of
+their parent ``fid``; they are not accepted as standalone primary datasets.
+TopSpin/NMR ``ser`` is intentionally unsupported.
+
+Known pulse-program names use dedicated layouts. For custom sequences the
+reader also infers common acquisition families from metadata; callers can pass
+``scheme_id=`` when inference is ambiguous. Rawdata is returned as complex
+ordered samples, not as reconstructed k-space. See the compatibility page in
+the documentation for behavior and current reconstruction limitations.

{brukerapi-0.2.6 → brukerapi-0.3.0}/README.rst

@@ -28,9 +28,9 @@ Load any **data set**:
 .. code-block:: python
 
     from brukerapi.dataset import Dataset
-    dataset = Dataset('{path}/2dseq')    # create data set, works for fid, 2dseq, rawdata.x
+    dataset = Dataset('{path}/2dseq')    # also supports fid, fid_proc.64, traj, and rawdata.jobN
     dataset.data                         # access data array
-    dataset.VisuCoreSize                 # get a value of a single parameter
+    dataset.get_value('VisuCoreSize')    # get a parameter value
 
 Load an entire **study**:
 
@@ -40,17 +40,7 @@ Load an entire **study**:
     study = Study('{path_to_study_folder}')
     dataset = study.get_dataset(exp_id='1', proc_id='1')
 
-    # get_dataset returns an empty dataset
-    # in order to load data into the data set, you can either use the context manager:
-
-    with dataset as d:
-        d.data                         # access data array
-        d.VisuCoreSize                 # get a value of a parameter
-
-    # or the load function
-    dataset.load()
-    dataset.data                       # access data array
-    dataset.VisuCoreSize               # get a value of a single parameter
+    dataset.data                         # Study loads datasets by default
 
 Load a parametric file:
 
@@ -60,8 +50,8 @@ Load a parametric file:
 
    parameters = JCAMPDX('path_to_scan/method')
    
-   TR = data.params["PVM_RepetitionTime"].value # This way
-   TR = data.get_value("PVM_RepetitionTime") # Or this way
+   TR = parameters.params["PVM_RepetitionTime"].value
+   TR = parameters.get_value("PVM_RepetitionTime")
 
 
 
@@ -76,6 +66,8 @@ Features
 * **Random access** for **fid** and **2dseq** data sets
 * **Split** operation implemented over **2dseq** data sets
 * **Filter** operation implemented over Bruker **folders** (allowing you to work with a subset of your study only)
+* ParaVision 5.1, 6.0.1, 7.0.0, and 360 metadata and binary-layout support
+* Metadata-based fallback inference for custom Cartesian, EPI, radial/UTE, spiral, ZTE, CSI, and spectroscopy sequences
 
 Examples
 ========
@@ -105,8 +97,7 @@ From source:
 
     git clone https://github.com/isi-nmr/brukerapi-python.git
     cd brukerapi-python
-    python setup.py build
-    python setup.py install
+    python -m pip install -e .[dev]
 
 Testing
 ========
@@ -115,107 +106,38 @@ data sets:
 
 * `BrukerAPI test data set (Bruker ParaVision v5.1) <https://doi.org/10.5281/zenodo.3899268>`_
 * `BrukerAPI test data set (Bruker ParaVision v6.0.1) <https://doi.org/10.5281/zenodo.3894651>`_
-* `bruker2nifti_qa data set <https://gitlab.com/naveau/bruker2nifti_qa>`_
+* BrukerAPI test data set for ParaVision v7.0.0 (Zenodo DOI collection ``10.5281/zenodo.4522220``)
+* `PV360 standard data <https://github.com/cecilyen/PV360_StdData>`_
+
+The corpus download is opt-in for local runs:
+
+.. code-block:: shell
+
+    python -m pytest test --download_test_data
+
+Without that flag, pytest uses any corpus already present under ``test/test_data`` and
+skips unavailable collections.
+
+File format reference
+=====================
+
+`Bruker ParaVision Raw Data Format
+<https://github.com/gdevenyi/brkraw-legacy/blob/main/FILE_FORMAT.md>`_ is the source of truth
+for file-format parsing, binary layouts, dataset typing, and metadata-driven acquisition
+scheme inference in this project.
 
 Compatibility
 =============
 
-The API was tested using various data sets obtained by **ParaVision 5.1**, **6.0.1** and **360**. It it is compatible
-with the following data set types from individual ParaVision versions.
-
-ParaVision v5.1
-"""""""""""""""
-Compatible data set types:
-
-* **fid**
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
-Compatible pulse sequences for **fid** data sets:
-
-* FLASH.ppg
-* MGE.ppg
-* MSME.ppg
-* RARE.ppg
-* FAIR_RARE.ppg
-* RAREVTR.ppg
-* RAREst.ppg
-* MDEFT.ppg
-* FISP.ppg
-* FLOWMAP.ppg
-* DtiStandard.ppg
-* EPI.ppg
-* FAIR_EPI.ppg
-* DtiEpi.ppg
-* T1_EPI.ppg
-* T2_EPI.ppg
-* T2S_EPI.ppg
-* SPIRAL.ppg
-* DtiSpiral.ppg
-* UTE.ppg
-* UTE3D.ppg
-* ZTE.ppg
-* CSI.ppg
-* FieldMap.ppg
-* NSPECT.ppg
-* PRESS.ppg
-* STEAM.ppg
-* igFLASH.ppg
-
-ParaVision v6.0.1 and v7.0.0
-"""""""""""""""""""""""""""""""
-Compatible data set types:
-
-* **fid**
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
-
-Compatible pulse sequences for **fid** data sets:
-
-* FLASH.ppg,
-* FLASHAngio.ppg
-* IgFLASH.ppg
-* MGE.ppg
-* MSME.ppg
-* RARE.ppg
-* FAIR_RARE.ppg
-* RAREVTR.ppg
-* RAREst.ppg
-* MDEFT.ppg
-* FISP.ppg
-* FLOWMAP.ppg
-* DtiStandard.ppg
-* EPI.ppg
-* FAIR_EPI.ppg
-* CASL_EPI.ppg
-* DtiEpi.ppg
-* T1_EPI.ppg
-* T2_EPI.ppg
-* T2S_EPI.ppg
-* SPIRAL.ppg
-* DtiSpiral.ppg
-* UTE.ppg
-* UTE3D.ppg
-* ZTE.ppg
-* CSI.ppg
-* FieldMap.ppg
-* SINGLEPULSE.ppg
-* NSPECT.ppg
-* EPSI.ppg
-* PRESS.ppg
-* STEAM.ppg
-* ISIS.ppg
-* CPMG.ppg
-* RfProfile.ppg
-
-
-ParaVision 360 v1.1 v3.0-v3.7
-"""""""""""""""""""""""""""""""""
-Reading rawdata is supported only in a basic form, no reshaping into k-space is supported at the moment.
-Compatible data set types:
-
-* **2dseq**
-* **rawdata.job0**
-* **rawdata.Navigator**
+Tested releases are ParaVision 5.1, 6.0.1, 7.0.0, and PV360 3.x. Supported
+primary binaries are ``fid``, ``fid_proc.64``, ``2dseq``, ``traj``,
+``rawdata.jobN``, and ``rawdata.Navigator``. Known ``fid.spiral``,
+``fid.navFid``, and ``fid.orig`` files are exposed as auxiliary subdatasets of
+their parent ``fid``; they are not accepted as standalone primary datasets.
+TopSpin/NMR ``ser`` is intentionally unsupported.
+
+Known pulse-program names use dedicated layouts. For custom sequences the
+reader also infers common acquisition families from metadata; callers can pass
+``scheme_id=`` when inference is ambiguous. Rawdata is returned as complex
+ordered samples, not as reconstructed k-space. See the compatibility page in
+the documentation for behavior and current reconstruction limitations.

{brukerapi-0.2.6 → brukerapi-0.3.0}/brukerapi/cli.py

@@ -141,7 +141,7 @@ def report(args):
     elif output is None:
         Dataset(input, add_parameters=["subject"]).report(props=args.props, verbose=args.verbose)
     # dataset to folder, or dataset to file
-    elif output.is_dir():
+    else:
         Dataset(input, add_parameters=["subject"]).report(path=output, props=args.props, verbose=args.verbose)
 
 

{brukerapi-0.2.6 → brukerapi-0.3.0}/brukerapi/config/properties_2dseq_core.json

@@ -143,12 +143,20 @@
     {
       "cmd": "#VisuCoreDataSlope.array",
       "conditions": []
+    },
+    {
+      "cmd": "#RECO_map_slope.array",
+      "conditions": []
     }
   ],
   "offset": [
     {
       "cmd": "#VisuCoreDataOffs.array",
       "conditions": []
+    },
+    {
+      "cmd": "#RECO_map_offset.array",
+      "conditions": []
     }
   ],
   "dim_type": [
@@ -169,4 +177,4 @@
       "conditions": ["@is_single_slice==False"]
     }
   ]
-}
+}

{brukerapi-0.2.6 → brukerapi-0.3.0}/brukerapi/config/properties_2dseq_custom.json

@@ -130,6 +130,18 @@
         "#VisuCorePosition.size[0]==1",
         "#VisuCoreDim==2"]
     },
+    {
+      "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], np.linalg.norm(#VisuCorePosition[1,:] - #VisuCorePosition[0,:])])",
+      "conditions": [
+        "#VisuCorePosition.size[0]>1",
+        "#VisuCoreDim==2"]
+    },
+    {
+      "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreFrameThickness])",
+      "conditions": [
+        "#VisuCorePosition.size[0]==1",
+        "#VisuCoreDim==2"]
+    },
     {
       "cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreExtent[2] / #VisuCoreSize[2]])",
       "conditions": [
@@ -253,13 +265,13 @@
       {
         "cmd": "datetime.datetime.strptime(#VisuStudyDate[1:-1], '%X %d %b %Y')",
         "conditions": [
-          "#VisuVersion==1"
+          "'T' not in #VisuStudyDate"
         ]
       },
       {
         "cmd": "datetime.datetime.strptime(#VisuStudyDate[1:-1], '%Y-%m-%dT%X,%f%z')",
         "conditions": [
-          "#VisuVersion==3"
+          "'T' in #VisuStudyDate"
         ]
       }
   ],
@@ -274,4 +286,4 @@
       "comment": "default value"
     }
   ]
-}
+}

{brukerapi-0.2.6 → brukerapi-0.3.0}/brukerapi/config/properties_fid_core.json

@@ -47,7 +47,73 @@
         "conditions": [
           "#ACQ_word_size=='_32_BIT'",
           "#BYTORDA=='little'",
-          ["#ACQ_sw_version",["<PV-360.1.1>"]]
+          "#ACQ_sw_version=='<PV-360.1.1>' or #ACQ_sw_version.value.startswith('<PV-360.3.')"
+        ]
+    },
+    {
+        "cmd": "np.dtype('i4').newbyteorder('>')",
+        "conditions": [
+          "#ACQ_word_size=='_32_BIT'",
+          "#BYTORDA=='big'",
+          "#ACQ_sw_version=='<PV-360.1.1>' or #ACQ_sw_version.value.startswith('<PV-360.3.')"
+        ]
+    },
+    {
+        "cmd": "np.dtype('i2').newbyteorder('<')",
+        "conditions": [
+          "#ACQ_word_size=='_16_BIT'",
+          "#BYTORDA=='little'",
+          "#ACQ_sw_version=='<PV-360.1.1>' or #ACQ_sw_version.value.startswith('<PV-360.3.')"
+        ]
+    },
+    {
+        "cmd": "np.dtype('i2').newbyteorder('>')",
+        "conditions": [
+          "#ACQ_word_size=='_16_BIT'",
+          "#BYTORDA=='big'",
+          "#ACQ_sw_version=='<PV-360.1.1>' or #ACQ_sw_version.value.startswith('<PV-360.3.')"
+        ]
+    },
+    {
+        "cmd": "np.dtype('i4').newbyteorder('<')",
+        "conditions": [
+          "#DTYPA in [0, 'Integer']",
+          "#BYTORDA=='little'"
+        ]
+    },
+    {
+        "cmd": "np.dtype('i4').newbyteorder('>')",
+        "conditions": [
+          "#DTYPA in [0, 'Integer']",
+          "#BYTORDA=='big'"
+        ]
+    },
+    {
+        "cmd": "np.dtype('f4').newbyteorder('<')",
+        "conditions": [
+          "#DTYPA in [1, 'Float']",
+          "#BYTORDA=='little'"
+        ]
+    },
+    {
+        "cmd": "np.dtype('f4').newbyteorder('>')",
+        "conditions": [
+          "#DTYPA in [1, 'Float']",
+          "#BYTORDA=='big'"
+        ]
+    },
+    {
+        "cmd": "np.dtype('f8').newbyteorder('<')",
+        "conditions": [
+          "#DTYPA in [2, 'Double']",
+          "#BYTORDA=='little'"
+        ]
+    },
+    {
+        "cmd": "np.dtype('f8').newbyteorder('>')",
+        "conditions": [
+          "#DTYPA in [2, 'Double']",
+          "#BYTORDA=='big'"
         ]
     }
   ],
@@ -96,7 +162,7 @@
       ]
     }
   ],
-  "acq_lenght": [
+  "acq_length": [
     {
       "cmd": "#ACQ_size.tuple[0] * @channels",
       "conditions": [
@@ -196,8 +262,7 @@
         ["#PULPROG[1:-1]",
           [
             "UTE.ppg",
-            "UTE3D.ppg",
-            "ZTE.ppg"
+            "UTE3D.ppg"
           ]
         ]
       ]
@@ -416,7 +481,7 @@
     },
     {
       "cmd": [
-        "#PVM_EncMatrix[0] * #PVM_EncMatrix[1] // #NSegments",
+        "#PVM_DigNp",
         "#PVM_EncNReceivers",
         "#NSegments",
         "#NI",
@@ -507,7 +572,7 @@
         "#PVM_EncNReceivers",
         "#ACQ_phase_factor",
         "#NI",
-        "NPro / ACQ_phase_factor",
+        "#NPro // #ACQ_phase_factor",
         "#NR"
       ],
       "conditions": [
@@ -617,7 +682,7 @@
     },
     {
       "cmd": [
-        "#PVM_EncMatrix[0]",
+        "#PVM_DigNp // (#PVM_EncMatrix[1] // #NSegments)",
         "#PVM_EncMatrix[1]",
         "#NI",
         "#NR",

{brukerapi-0.2.6 → brukerapi-0.3.0}/brukerapi/config/properties_fid_custom.json

@@ -52,13 +52,13 @@
     {
         "cmd": "datetime.datetime.strptime(#ACQ_time,'<%Y-%m-%dT%X,%f%z>')",
         "conditions": [
-          "#ACQ_sw_version=='<PV 6.0.1>'"
+          "'T' in #ACQ_time"
         ]
     },
     {
         "cmd": "datetime.datetime.strptime(#ACQ_time,'<%H:%M:%S %d %b %Y>')",
         "conditions": [
-          "#ACQ_sw_version=='<PV 5.1>'"
+          "'T' not in #ACQ_time"
         ]
     }
   ],
@@ -88,4 +88,4 @@
         "unit": "ms"
     }
   ]
-}
+}

{brukerapi-0.2.6 → brukerapi-0.3.0}/brukerapi/config/properties_rawdata_core.json

@@ -77,7 +77,7 @@
   ],
   "job_desc": [
     {
-      "cmd": "#ACQ_jobs.primed_dict(7)['<{}>'.format(@subtype)]",
+      "cmd": "#ACQ_jobs.primed_dict(-1)['<{}>'.format(@subtype)]",
       "conditions": [
         ["#ACQ_sw_version",["<PV-360.1.1>"]]
       ]
@@ -112,6 +112,12 @@
     }
   ],
   "shape_storage": [
+    {
+      "cmd": "(@job_desc[0],) + (#PVM_EncNReceivers,) + (@job_desc[6],)",
+      "conditions": [
+        "#ACQ_sw_version.value.startswith('<PV-360.3.')"
+      ]
+    },
     {
       "cmd": "(@job_desc[0],) + (#PVM_EncNReceivers,) + (@job_desc[3],)",
       "conditions": []

{brukerapi-0.2.6 → brukerapi-0.3.0}/brukerapi/config/properties_traj_core.json

@@ -14,8 +14,7 @@
           [
             "UTE.ppg",
             "UTE3D.ppg",
-            "IgUTE.ppg",
-            "ZTE.ppg"
+            "IgUTE.ppg"
           ]
         ]
       ]

brukerapi-0.3.0/brukerapi/data.py

@@ -0,0 +1,7 @@
+class DataRandomAccess:
+    def __init__(self, dataset):
+        self._dataset = dataset
+        self._schema = dataset._schema
+
+    def __getitem__(self, key):
+        return self._schema.ra(key)